Problems in gene clustering based on gene expression data

Journal of Multivariate Analysis

Volumn 90, Issue 1 SPEC. ISS., 2004, Pages 44-66

  Bryan, Jenny ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Bootstrap; Cluster analysis; Confidence; Microarrays

Indexed keywords

EID: 20444442286     PISSN: 0047259X     EISSN: 10957243     Source Type: Journal    
DOI: 10.1016/j.jmva.2004.02.011     Document Type: Article

References (29)

1. J. Bryan, Gene classification based on deletion set studies, Refereed abstract and talk for Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics available from author's websitc at hajek.stat.ubc.ca/~jenny;
2. K. Baetz, L. McHardy, K. Gable, T. Tarling, D. Rebérioux, J. Bryan, T. Dunn, P. Hieter, M. Roberge, Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action, in Proc. Natl. Acad. Sci. in press.
3. J. Bryan, K.S. Pollard, M.J. van der Laan, Paired and unpaired comparison and clustering with gene expression data (special issue on bioinformatics), Statist. Sinica 12 (1) (2002) 87-110.
4. CAMDA, 2002, http://www.camda.duke.edu.
5. R. Cormack, A review of classification, J. Roy. Statist. Soc. Ser. A 134 (3) (1971) 321-367.
6. S. Dudoit, J. Fridlyand, A prediction-based resampling method for estimating the number of clusters in a dataset, Genome Biol. 3 (7) (2002) 0036.1-0036.21.
7. B. Durbin, J. Hardin, D. Hawkins, D. Rocke, A variance-stabilizing transformation for gene-expression microarray data, Bioinformatics 18 (2002) S105-S110.
8. B. Efron, E. Halloran, S. Holmes, Bootstrap confidence levels for phylogenetic trees, Proc. Nat. Acad. Sci. 93 (1996) 13429-13434.
9. B. Efron, R. Tibshirani, The problem of regions, Ann. Statist. 26 (5) (1998) 1687-1718.
10. M. Eisen, P. Spellman, P. Brown, D. Botstein, Cluster analysis and display of genome-wide expression patterns, Proc. Nat. Acad. Sci. 95 (1998) 14863-14868.
11. B. Everitt, Cluster Analysis, Heinemann Educational Books, London, 1974.
12. B.S. Everitt, S. Landau, M. Leese, Cluster Analysis, Arnold, London, 2001.
13. J. Felsenstein, Confidence limits on phylogenies: an approach using the bootstrap, Evolution 39 (4) (1985) 783-791.
14. T. Hastie, R. Tibshirani, J. Friedman, The Elements of Statistical Learning, Springer, New York, 2001.
15. http://www.bioconductor.org.
16. W. Huber, A. von Heydebreck, H. Sueltmann, A. Poustka, M. Vingron, Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Bioinformatics 18 (2002) S96-S104.
17. R. Ihaka, R. Gentleman, R: A language for data analysis and graphics, J. Comput. Graph. Statist. 5 (3) (1996) 299-314.
18. R.A. Irizarry, L. Gautier, L.M. Cope, An r package for analyses of affymetrix oligonucleotide arrays, in: G. Parmigiani, E. Garett, R. Irizarry, S. Zeger (Eds.), The Analysis of Gene Expression Data: Methods and Software, Statistics for Biology and Health, Springer, New York, 2003 (Chapter 4).
19. R.A. Johndon, D. Wichern, Applied Multivariate Statistical Analysis, Prentice-Hall, Englewood Cliffs, NJ, 2002.
20. L. Kaufman, P. Roussceuw, Finding Groups in Data: An Introduction to Cluster Analysis, Wiley, New York, 1990.
21. M. Kendall, Discrimination and classification, in: P. Krishnaiah (Ed.), Proceedings of Symposium Multivariate Analysis, Dayton, Ohio, Academic Press, New York, 1966, pp. 165-185.
22. M.K. Kerr, G. Churchill, Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments, Proc. Nat. Acad. Sci. 98 (2001) 8961-8965.
23. G.W. Milligan, S. Soon, L.M. Sokol, The effect of cluster size, dimensionality, and the number of clusters on recovery of true cluster structure, IEEE Trans. Pattern Anal. Mach. Intell. PAMI-5 (1983) 40-47.
24. K.S. Pollard, M.J. van der Laan, Statistical inference for simultaneous clustering of gene expression data, Math. Biosci. 176 (2002) 99-121.
25. C. Pritchard, L. Hsu, J. Delrow, P. Nelson, Project normal: defining normal variance in mouse gene expression, Proc. Nat. Acad. Sci. 98 (23) (2001) 13266-13271.
26. W. Rand, Objective criteria for the evaluation of clustering methods, J. Amer. Statist. Assoc. 66 (1971) 846-850.
27. R. Tibshirani, W. Guenther, T. Hasite, Estimating the number of clusters in a data set via the gap statistic, J. Roy. Statist. Soc. Ser. B 63 (2001) 411-423.
28. M.J. van der Laan, J. Bryan, Gene expression analysis with the parametric bootstrap, Biostatistics 2 (4) (2001) 445-461.
29. J.C. Wakefield, C. Zhuo, S.G. Self, Modelling gene expression data over time: curve clustering with informative prior distributions, Bayesian Statist. 7 (2003) 711-722.